Here are the ones I found. Let me know if I missed any. I divided them up by franchise to make it easier.

Iron Man
-Howard Stark helped created the tech to create him and was directly involved in much operational planning and even missions
-Stark Industries responsible for most of the tech in the film
-Rogers attends a Stark Expo
-Shield made of Vibranium- what Tony is able to reproduce with his fathers clues in IM2
-Howard Stark finds the lost Tesseract at the end

Thor
-Tesseract a weapon left on earth by Odin during his battle with the Frost Giants in 965 AD in Norway (as shown in Thor)
-Yggdrasil wall art hides the Tesseract
-Asgardians were the "Gods" referenced throughout the film
-When the Tesseract reveals its true powers to Red Skull (before consuming him) the heavens are shown much like in Thor

Hulk
-Red Skulls deformed appearance is explained by his body's rejection of the serum because he was not worthy. It also drives him even madder. This is exactly what happens to Blonsky/Abomination in The Incredible Hulk.
-Super Soldier Serum is administered in a very similar way as it is to Blonsky in Hulk.

SHIELD
-Set up elaborate attempt to confuse Steve Rogers that it's still the 1940s in order to ease him into the present.
-Nick Fury appears at the end to tell him the truth.

General
-Stan Lee cameoed as a military officer at a Medal of Valor presentation for Steve, that he decides not to attend in order to keep fighting.
-Arnim Zola is first introduced as a giant distorted face on a screen
-Red Skull mentions that "the Fuhrer is too busy digging for trinkets in the desert" to look for a much more powerful item like the Tesseract. A direct reference to "Raiders of the Lost Ark" (which Johnston worked on- and borrowed from heavily in this film)
-Red Skull's death at the hands of the Tesseract was very similar to how the Lost Ark killed the Nazis in "Raiders of the Lost Ark"